sl-shared-assets 3.0.0rc9__py3-none-any.whl → 3.0.0rc10__py3-none-any.whl

sl_shared_assets/data_classes/configuration_data.py

@@ -44,7 +44,7 @@ class ExperimentState:
     automatically enabled. Specifically, if the experiment state supports running linearized Virtual Reality track, the 
     system will enable lick guidance for this many trials at the beginning of the experiment state and automatically 
     disable it for the following trials."""
-    failed_trial_threshold: int
+    recovery_failed_trial_threshold: int
     """Specifies the number of failed (non-rewarded) non-guided trials (laps), after which the system will re-enable 
     guidance for the 'recovery_guided_trials' number of following trials. For this to take effect, the trials must be 
     failed this many times in a row."""
@@ -122,7 +122,7 @@ class MesoscopeExperimentConfiguration(YamlConfig):
                 system_state_code=1,
                 state_duration_s=30,
                 initial_guided_trials=0,
-                failed_trial_threshold=0,
+                recovery_failed_trial_threshold=0,
                 recovery_guided_trials=0,
             ),
             "experiment": ExperimentState(
@@ -130,7 +130,7 @@ class MesoscopeExperimentConfiguration(YamlConfig):
                 system_state_code=2,
                 state_duration_s=120,
                 initial_guided_trials=3,
-                failed_trial_threshold=6,
+                recovery_failed_trial_threshold=6,
                 recovery_guided_trials=3,
             ),
             "cooldown": ExperimentState(
@@ -138,7 +138,7 @@ class MesoscopeExperimentConfiguration(YamlConfig):
                 system_state_code=1,
                 state_duration_s=15,
                 initial_guided_trials=1000000,
-                failed_trial_threshold=0,
+                recovery_failed_trial_threshold=0,
                 recovery_guided_trials=0,
             ),
         }

sl_shared_assets/data_classes/configuration_data.pyi

@@ -24,7 +24,7 @@ class ExperimentState:
     system_state_code: int
     state_duration_s: float
     initial_guided_trials: int
-    failed_trial_threshold: int
+    recovery_failed_trial_threshold: int
     recovery_guided_trials: int
 
 @dataclass()

sl_shared_assets/data_classes/runtime_data.py

@@ -205,10 +205,6 @@ class ZaberPositions(YamlConfig):
     Zaber motor positions across consecutive runtimes for the same project and animal combination.
 
     Notes:
-        The HeadBar axis (connection) also manages the motor that moves the running wheel along the x-axis. While the
-        motor itself is not part of the HeadBar assembly, it is related to positioning the mouse in the VR system. This
-        is in contrast to the LickPort group, which is related to positioning the lick tube relative to the mouse.
-
         All positions are saved using native motor units. All class fields initialize to default placeholders that are
         likely NOT safe to apply to the VR system. Do not apply the positions loaded from the file unless you are
         certain they are safe to use.
@@ -226,13 +222,12 @@ class ZaberPositions(YamlConfig):
     """The absolute position, in native motor units, of the HeadBar roll-axis motor."""
     lickport_z: int = 0
     """The absolute position, in native motor units, of the LickPort z-axis motor."""
-    lickport_x: int = 0
-    """The absolute position, in native motor units, of the LickPort x-axis motor."""
     lickport_y: int = 0
     """The absolute position, in native motor units, of the LickPort y-axis motor."""
+    lickport_x: int = 0
+    """The absolute position, in native motor units, of the LickPort x-axis motor."""
     wheel_x: int = 0
-    """The absolute position, in native motor units, of the running wheel platform x-axis motor. Although this motor is
-    not itself part of the HeadBar assembly, it is controlled through the HeadBar controller port."""
+    """The absolute position, in native motor units, of the running wheel platform x-axis motor."""
 
 
 @dataclass()
@@ -240,9 +235,9 @@ class MesoscopePositions(YamlConfig):
     """Stores real and virtual Mesoscope objective positions reused between experiment sessions that use the
     Mesoscope-VR system.
 
-    Primarily, the class is used to help the experimenter to position the Mesoscope at the same position across
+    Primarily, the class is used to help the experimenter to position the Mesoscope on the same imaging plane across
     multiple imaging sessions. It stores both the physical (real) position of the objective along the motorized
-    X, Y, Z, and Roll axes and the virtual (ScanImage software) tip, tilt, and fastZ focus axes.
+    X, Y, Z, and Roll axes, and the virtual (ScanImage software) tip, tilt, and fastZ focus axes.
 
     Notes:
         Since the API to read and write these positions automatically is currently not available, this class relies on
@@ -250,16 +245,18 @@ class MesoscopePositions(YamlConfig):
     """
 
     mesoscope_x: float = 0.0
-    """The X-axis position, in centimeters, of the Mesoscope objective used during session runtime."""
+    """The X-axis position, in centimeters, of the Mesoscope objective."""
     mesoscope_y: float = 0.0
-    """The Y-axis position, in centimeters, of the Mesoscope objective used during session runtime."""
+    """The Y-axis position, in centimeters, of the Mesoscope objective."""
     mesoscope_roll: float = 0.0
-    """The Roll-axis position, in degrees, of the Mesoscope objective used during session runtime."""
+    """The Roll-axis position, in degrees, of the Mesoscope objective."""
     mesoscope_z: float = 0.0
-    """The Z-axis position, in centimeters, of the Mesoscope objective used during session runtime."""
+    """The Z-axis position, in centimeters, of the Mesoscope objective."""
     mesoscope_fast_z: float = 0.0
-    """The Fast-Z-axis position, in micrometers, of the Mesoscope objective used during session runtime."""
+    """The Fast-Z-axis (virtual Z) position, in micrometers."""
     mesoscope_tip: float = 0.0
-    """The Tilt-axis position, in degrees, of the Mesoscope objective used during session runtime."""
+    """The Tilt-axis (software) position, in degrees.."""
     mesoscope_tilt: float = 0.0
-    """The Tip-axis position, in degrees, of the Mesoscope objective used during session runtime."""
+    """The Tip-axis (software) position, in degrees."""
+    laser_power_mw: float = 0.0
+    """The excitation laser power delivered to the sample, in milliwatts."""

sl_shared_assets/data_classes/runtime_data.pyi

@@ -106,10 +106,6 @@ class ZaberPositions(YamlConfig):
     Zaber motor positions across consecutive runtimes for the same project and animal combination.
 
     Notes:
-        The HeadBar axis (connection) also manages the motor that moves the running wheel along the x-axis. While the
-        motor itself is not part of the HeadBar assembly, it is related to positioning the mouse in the VR system. This
-        is in contrast to the LickPort group, which is related to positioning the lick tube relative to the mouse.
-
         All positions are saved using native motor units. All class fields initialize to default placeholders that are
         likely NOT safe to apply to the VR system. Do not apply the positions loaded from the file unless you are
         certain they are safe to use.
@@ -123,8 +119,8 @@ class ZaberPositions(YamlConfig):
     headbar_pitch: int = ...
     headbar_roll: int = ...
     lickport_z: int = ...
-    lickport_x: int = ...
     lickport_y: int = ...
+    lickport_x: int = ...
     wheel_x: int = ...
 
 @dataclass()
@@ -132,9 +128,9 @@ class MesoscopePositions(YamlConfig):
     """Stores real and virtual Mesoscope objective positions reused between experiment sessions that use the
     Mesoscope-VR system.
 
-    Primarily, the class is used to help the experimenter to position the Mesoscope at the same position across
+    Primarily, the class is used to help the experimenter to position the Mesoscope on the same imaging plane across
     multiple imaging sessions. It stores both the physical (real) position of the objective along the motorized
-    X, Y, Z, and Roll axes and the virtual (ScanImage software) tip, tilt, and fastZ focus axes.
+    X, Y, Z, and Roll axes, and the virtual (ScanImage software) tip, tilt, and fastZ focus axes.
 
     Notes:
         Since the API to read and write these positions automatically is currently not available, this class relies on
@@ -148,3 +144,4 @@ class MesoscopePositions(YamlConfig):
     mesoscope_fast_z: float = ...
     mesoscope_tip: float = ...
     mesoscope_tilt: float = ...
+    laser_power_mw: float = ...

sl_shared_assets/data_classes/session_data.py

@@ -498,12 +498,12 @@ class SessionData(YamlConfig):
         # Returns the initialized SessionData instance to caller
         return instance
 
-    def mark_initialization(self) -> None:
-        """Ensures that the 'nk.bin' marker file is removed from the session's raw_dat folder.
+    def runtime_initialized(self) -> None:
+        """Ensures that the 'nk.bin' marker file is removed from the session's raw_data folder.
 
         This marker is generated as part of the SessionData initialization (creation) process to mark sessions that did
-        not fully initialize during runtime. Call this method after fully initializing the data acquisition runtime
-        control class to ensure that the session is not marker for automated deletion upon runtime completion.
+        not fully initialize during runtime. This service method is designed to be called by the inner runtime control
+        functions and classes of the sl-experiment library and generally should not be called by end-users.
         """
         self.raw_data.nk_path.unlink(missing_ok=True)
 

sl_shared_assets/data_classes/session_data.pyi

@@ -192,12 +192,12 @@ class SessionData(YamlConfig):
             FileNotFoundError: If the 'session_data.yaml' file is not found under the session_path/raw_data/ subfolder.
 
         """
-    def mark_initialization(self) -> None:
-        """Ensures that the 'nk.bin' marker file is removed from the session's raw_dat folder.
+    def runtime_initialized(self) -> None:
+        """Ensures that the 'nk.bin' marker file is removed from the session's raw_data folder.
 
         This marker is generated as part of the SessionData initialization (creation) process to mark sessions that did
-        not fully initialize during runtime. Call this method after fully initializing the data acquisition runtime
-        control class to ensure that the session is not marker for automated deletion upon runtime completion.
+        not fully initialize during runtime. This service method is designed to be called by the inner runtime control
+        functions and classes of the sl-experiment library and generally should not be called by end-users.
         """
     def _save(self) -> None:
         """Saves the instance data to the 'raw_data' directory of the managed session as a 'session_data.yaml' file.

sl_shared_assets/tools/ascension_tools.py

@@ -227,7 +227,7 @@ def ascend_tyche_data(root_directory: Path) -> None:
                 )
 
                 # Since this runtime reprocesses already acquired data, marks the session as fully initialized.
-                session_data.mark_initialization()
+                session_data.runtime_initialized()
 
                 # Moves the data from the old hierarchy to the new hierarchy. If the process runs as expected, and
                 # fully empties the source acquisition folder, destroys the folder. Otherwise, notifies the user that

{sl_shared_assets-3.0.0rc9.dist-info → sl_shared_assets-3.0.0rc10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 3.0.0rc9
+Version: 3.0.0rc10
 Summary: Provides data acquisition and processing assets shared between Sun (NeuroAI) lab libraries.
 Project-URL: Homepage, https://github.com/Sun-Lab-NBB/sl-shared-assets
 Project-URL: Documentation, https://sl-shared-assets-api-docs.netlify.app/

{sl_shared_assets-3.0.0rc9.dist-info → sl_shared_assets-3.0.0rc10.dist-info}/RECORD

@@ -5,12 +5,12 @@ sl_shared_assets/cli.pyi,sha256=8ZJK56_jh2QlF3XCN6c7fI6Z022XtehB0eCrQDJbAsU,5515
 sl_shared_assets/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sl_shared_assets/data_classes/__init__.py,sha256=SUDN7gFngUPEa7Da_G0PjXwnF9Q0S4EgvjpKe3KSr5g,1852
 sl_shared_assets/data_classes/__init__.pyi,sha256=J-tUXAtGEasacVU1qGFFksvfB1tFdEO-GKs90vSTAcg,2022
-sl_shared_assets/data_classes/configuration_data.py,sha256=73IP9e8bESHbYlr0sCCLktU3JScofuSTuLE8N4MIwjs,35389
-sl_shared_assets/data_classes/configuration_data.pyi,sha256=Jg4TmrDjEBtQn7zH0140-6pQ1J9ljSuzC0tiysx4qBM,10772
-sl_shared_assets/data_classes/runtime_data.py,sha256=O98BZg7i7cEUlpIE16JswKOwQNRsS5RxVdBzXYvAw00,16543
-sl_shared_assets/data_classes/runtime_data.pyi,sha256=i8CuZd9p0Nu43xhpE62pB07AiovZIgtMZYN5wQjz-r0,6861
-sl_shared_assets/data_classes/session_data.py,sha256=nvGW8TagsGmxH3Eh63zosKHJAfOT4U_2ukfxy3frum8,45575
-sl_shared_assets/data_classes/session_data.pyi,sha256=QEoxKdcaa0lwJ8Bv4rsvAiC32lwpagcsnsnRK1x0AqA,14152
+sl_shared_assets/data_classes/configuration_data.py,sha256=bTkfJqQfNdw-vnsZfzLBE_rLFR_YoiYM3BZQt08Syp4,35425
+sl_shared_assets/data_classes/configuration_data.pyi,sha256=9X06Zsuj2p3XTOdb651rBnZ2RYdRzlv1F7KiMOtNF_8,10781
+sl_shared_assets/data_classes/runtime_data.py,sha256=MwNe_Ilg-DwfgboYafizRj--05z85WsIHQimxDUqI0w,15937
+sl_shared_assets/data_classes/runtime_data.pyi,sha256=BX4sPgr47pitg24N2fvCIFxjG_s9DkqCimF8hiO7Jmo,6545
+sl_shared_assets/data_classes/session_data.py,sha256=yUcHYajAv0SKir2HOHYSMkXkusFL5XP_KfkzzvkmnX0,45576
+sl_shared_assets/data_classes/session_data.pyi,sha256=hNNElZHOe5hlQAStkNqkYYl1UbfGh88LchYjBIqdreY,14153
 sl_shared_assets/data_classes/surgery_data.py,sha256=qsMj3NkjhylAT9b_wHBY-1XwTu2xsZcZatdECmkA7Bs,7437
 sl_shared_assets/data_classes/surgery_data.pyi,sha256=rf59lJ3tGSYKHQlEGXg75MnjajBwl0DYhL4TClAO4SM,2605
 sl_shared_assets/server/__init__.py,sha256=w7y73RXXjBrWQsjU5g1QNCv_gsXDYnHos3NpOoR2AHA,452
@@ -21,7 +21,7 @@ sl_shared_assets/server/server.py,sha256=MGk1v49aEFeIChMDsiR7CXjVkWwDpD9kA1TK0fw
 sl_shared_assets/server/server.pyi,sha256=5Yxq4txhjtd9w-6U9fPehzMeIZL5GcprVCHd9mPP6FI,15113
 sl_shared_assets/tools/__init__.py,sha256=NktXk62E_HHOrO_93z_MVmSd6-Oir3mE4xE9Yr8Qa7U,682
 sl_shared_assets/tools/__init__.pyi,sha256=0UXorfCXXmHQOP5z7hODpsqEX0DAkOta5VZqN6FSS-w,623
-sl_shared_assets/tools/ascension_tools.py,sha256=XdJC3nibtgqpmH0KG6Q-YZkOLTK3TexZHWVglqW0pl4,14595
+sl_shared_assets/tools/ascension_tools.py,sha256=1cDs6Nx3woL9UPESQBpMbP7mC5URxCdPmjpU_GN87c4,14595
 sl_shared_assets/tools/ascension_tools.pyi,sha256=c-SI9TYJ1vmJXMV2pSW9Nri4mlySF8MtXqrvRvz5C8s,3705
 sl_shared_assets/tools/packaging_tools.py,sha256=QikjeaE_A8FyVJi3cnWLeW-hUXy1-FF1N23muA5VfT4,7526
 sl_shared_assets/tools/packaging_tools.pyi,sha256=vgGbAQCExwg-0A5F72MzEhzHxu97Nqg1yuz-5P89ycU,3118
@@ -29,8 +29,8 @@ sl_shared_assets/tools/project_management_tools.py,sha256=Z_U0R26w9Le1O-u66gyF5C
 sl_shared_assets/tools/project_management_tools.pyi,sha256=4kok98nOZ4KnT-Sg-ZCZYg-WIM5qZqiyK8g1XiiDjHM,10375
 sl_shared_assets/tools/transfer_tools.py,sha256=J26kwOp_NpPSY0-xu5FTw9udte-rm_mW1FJyaTNoqQI,6606
 sl_shared_assets/tools/transfer_tools.pyi,sha256=FoH7eYZe7guGHfPr0MK5ggO62uXKwD2aJ7h1Bu7PaEE,3294
-sl_shared_assets-3.0.0rc9.dist-info/METADATA,sha256=ld-V567zlZD-KHbtRdqSIMivD--AjX_VW-l9WV4Wyuk,49309
-sl_shared_assets-3.0.0rc9.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-sl_shared_assets-3.0.0rc9.dist-info/entry_points.txt,sha256=UmO1rl7ly9N7HWPwWyP9E0b5KBUStpBo4TRoqNtizDY,430
-sl_shared_assets-3.0.0rc9.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-sl_shared_assets-3.0.0rc9.dist-info/RECORD,,
+sl_shared_assets-3.0.0rc10.dist-info/METADATA,sha256=OpcKZWppCyDoGafIiWowtf9p9HZcdbV2lEuQPADmAqY,49310
+sl_shared_assets-3.0.0rc10.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+sl_shared_assets-3.0.0rc10.dist-info/entry_points.txt,sha256=UmO1rl7ly9N7HWPwWyP9E0b5KBUStpBo4TRoqNtizDY,430
+sl_shared_assets-3.0.0rc10.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+sl_shared_assets-3.0.0rc10.dist-info/RECORD,,